plotPoset: Plot a poset.

In OncoSimulR: Forward Genetic Simulation of Cancer Progression with Epistasis

Description

Plot a poset. Optionally add a root and change names of nodes.

Usage

plotPoset(x, names = NULL, addroot = FALSE, box = FALSE, ...)

Arguments

x	A poset. A matrix with two columns where, in each row, the first column is the ancestor and the second the descendant. Note that there might be multiple rows with the same ancestor, and multiple rows with the same descendant. See poset.
names	If not NULL, a vector of names for the nodes, with the same length as the total number of nodes in a poset (which need not be the same as the number of rows; see poset). If addroot = TRUE, then 1 + the number of nodes in the poset.
addroot	Add a "Root" node to the graph?
box	Should the graph be placed inside a box?
...	Additional arguments to plot (actually, plot.graphNEL in the Rgraphviz package

).

Details

The poset is converted to a graphNEL object.

Value

A plot is produced.

Author(s)

Ramon Diaz-Uriarte

See Also

examplePosets, poset

Examples

data(examplePosets)
plotPoset(examplePosets[["p1101"]])

## If you will be using that poset a lot, maybe simpler if

poset701 <- examplePosets[["p701"]]
plotPoset(poset701, addroot = TRUE)

## Compare to Pancreatic cancer figure in Gerstung et al., 2011

plotPoset(poset701,
          names = c("KRAS", "SMAD4", "CDNK2A", "TP53",
                     "MLL3","PXDN", "TGFBR2"))

## If you want to show Root explicitly do

plotPoset(poset701, addroot = TRUE,
          names = c("Root", "KRAS", "SMAD4", "CDNK2A", "TP53",
                     "MLL3","PXDN", "TGFBR2"))


## Of course, names are in the order of nodes, so KRAS is for node 1,
##   etc, but the order of entries in the poset does not matter:

poset701b <- poset701[nrow(poset701):1, ]

plotPoset(poset701b,
          names = c("KRAS", "SMAD4", "CDNK2A", "TP53",
                     "MLL3","PXDN", "TGFBR2"))

OncoSimulR documentation built on Nov. 8, 2020, 8:31 p.m.